Phylogenetic analysis of a Bean yellow mosaic virus isolate from Iran and selecting the phylogenetic marker by comparing the individual genes and complete genome trees of BYMV isolates

Baradar, Ali; Hosseini, Ahmad; Ratti, Claudio; Hosseini, Samin

doi:10.1016/j.pmpp.2021.101632

Cited by 2 publications

(3 citation statements)

References 51 publications

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“…The selection of an appropriate phylogenetic gene marker was previously performed for other viruses by different authors. As an example, Tomimura et al [46] indicated the NIb-VPg regions as phylogenetic markers for turnip mosaic virus, and Baradar et al [47] reported that the NIb, Nib, and VPg genes can be used as evolutionary markers for bean yellow mosaic virus; both of these viruses belong to the Potyvirus genus. In this study, the ML-based IQtree and BI-based MrBayes programs were used for the reconstruction of full genome and individual gene trees and all fully sequenced GVA isolates were classified and compared to Alabi et al [19].…”

Section: Discussionmentioning

confidence: 99%

“…Most available isolates in public databases are partially sequenced and virologists are obliged to use partial genomes or individual genes for phylogenetic studies. As such, to avoid unbiased classification, phylogenetic studies should be based on either phylogenetic gene marker(s) or on a multigene dataset, instead of just one random gene (47). This study is the first to determine a marker gene for GVA phylogenetic and evolutionary analysis, and the methodology and the results here described can be used for further research on phylogenetic analysis, evolution history, epidemiology, etiology, and control measures of GVA, taken as the type species of the Vitivirus genus, but also for other viruses of grapevine.…”

Section: Discussionmentioning

confidence: 99%

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Phylogenetic Marker Selection and Protein Sequence Analysis of the ORF5 Gene Product of Grapevine Virus A

Rastgou

Roumi

Noris

et al. 2022

Plants

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Grapevine virus A (GVA), the type species of the Vitivirus genus, is one of the causal agents of the Kober stem grooving disease of the rugose wood complex and one of the most frequently detected viruses in grapevine. There is little information on GVA gene(s) marker useful for phylogenetic analysis. To this aim, a total of 403 leaf samples were collected from vineyards of East and West Azarbaijan provinces in the Northwestern provinces of Iran during 2014–2016 and tested by DAS-ELISA and RT-PCR using ORF5-specific primers. GVA was detected in 56 symptomatic samples, corresponding to 14% of infection, while it was not detected in asymptomatic samples. The ORF5 (p10) protein sequence of eight Iranian isolates was compared to other vitiviruses, showing that the most conserved region resides in the N-terminus, carrying an arginine-rich motif followed by a zinc-finger motif. Next, to define a robust phylogenetic marker representative of the whole genome sequence suitable for phylogenetic and evolutionary studies, phylogenetic trees based on the full genome sequences of all the available GVA isolates and on individual genomic regions were constructed and compared. ORF1, which encodes the RNA-dependent RNA polymerase, was found to be the best phylogenetic marker for GVA classification and evolution studies. These results can be used for further research on phylogenetic analyses, evolution history, epidemiology, and etiology of rugose wood complex, and to identify control measures against GVA and other vitiviruses.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Phylogenetic Marker Selection and Protein Sequence Analysis of the ORF5 Gene Product of Grapevine Virus A

Rastgou

Roumi

Noris

et al. 2022

Plants

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“…Bean yellow mosaic virus (BYMV) is one of the most important legume-infecting potyviruses, although its wide host range also includes various monocots and dicots within both domesticated and wild plant species [7,8]. Based on studies of BYMV molecular variability, at least nine molecular groups have been identified [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Molecular Characteristics and Biological Properties of Bean Yellow Mosaic Virus Isolates from Slovakia

Mrkvová,

Kemenczeiová,

Achs

et al. 2024

Horticulturae

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Analysis of the viromes of three symptomatic Fabaceae plants, i.e., red clover (Trifolium pratense L.), pea (Pisum sativum L.), and common bean (Phaseolus vulgaris L.), using high-throughput sequencing revealed complex infections and enabled the acquisition of complete genomes of a potyvirus, bean yellow mosaic virus (BYMV). Based on phylogenetic analysis, the Slovak BYMV isolates belong to two distinct molecular groups, i.e., VI (isolate FA40) and XI (isolates DAT, PS2). Five commercial pea genotypes (Alderman, Ambrosia, Gloriosa, Herkules, Senator) were successfully infected with the BYMV-PS2 inoculum and displayed similar systemic chlorotic mottling symptoms. Relative comparison of optical density values using semi-quantitative DAS-ELISA revealed significant differences among virus titers in one of the infected pea genotypes (Ambrosia) when upper fully developed leaves were tested. Immunoblot analysis of systemically infected Alderman plants showed rather uneven virus accumulation in different plant parts. The lowest virus accumulation was repeatedly detected in the roots, while the highest was in the upper part of the plant stem.

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Phylogenetic analysis of a Bean yellow mosaic virus isolate from Iran and selecting the phylogenetic marker by comparing the individual genes and complete genome trees of BYMV isolates

Cited by 2 publications

References 51 publications

Phylogenetic Marker Selection and Protein Sequence Analysis of the ORF5 Gene Product of Grapevine Virus A

Phylogenetic Marker Selection and Protein Sequence Analysis of the ORF5 Gene Product of Grapevine Virus A

Molecular Characteristics and Biological Properties of Bean Yellow Mosaic Virus Isolates from Slovakia

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